Small molecule chemical inhibitors of biological systems are powerful tools for probing complex biological processes and they also hold the promise of new therapies. Not surprisingly, there has been much effort invested into adapting assays for high throughput screens to identify such molecules that affect important biological processes. In this regard, cell-based phenotypic assays are particularly powerful as they make few assumptions about mechanism and the read out is likely to be biologically relevant. We have developed a high throughput assay system that detects the effect of the HIV protein, Nef, on the cell surface expression of the cellular protein, MHC-I, which is required for immune recognition of infected cells. Nef reduces the expression of this molecule to evade the immune response and establish a chronic infection. Inhibitors of this process would aid efforts to understand the mechanism by which Nef affects MHC-I expression and would have therapeutic potential. PUBLIC HEALTH RELEVANCE: Although currently available anti-HIV drugs effectively prevent the development of disease in many affected individuals, they do not cure disease. It has been proposed that residual cellular reservoirs that are not affected by current therapies are responsible for re-establishing high viral loads. Inhibitors of the Nef protein may improve the treatment of HIV-infected people by allowing the immune system to more efficiently identify and eradicate infected cells.